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91 Cards in this Set

Have one end that will dissolve in water and one end that wil disoolve in a nonpolar environment

Hydrogen Bonds

Hydrogen atom covalently bonded to one electronegative atom interacts with another electronegative atom

In SDS-PAGE, separation takes place on the bases of:

The sieving action of the gel, since all particles have approx the same charge/mass ratio, but dif. masses

A single water molecule can participate in up to __ H-bonds

4

The dominant interaction that drives a water-soluble protein to fold is:

The hydrophobic interaction

Which substance would be a suitable buffer at pH 5.0?

one with a pKa of ~ 5.0

Two amino acids frequently found in reverse turns are:

glycine and proline

In isoelectric focusing gel electrophoresis:

there is a pH gradient that parallels the electric fild gradient

True statements about water and/or H-bonds

1. H-atoms of water each bear a partial pos charge
2. H-bonds can form b/w diff parts of polypeptide chain
3. H-bonds are relatively weak compared to covalent bonds.
4. H-bonds in water contribute to its cohesiveness

Procedure necessary to test whether amino acid sequence of ibonuclease contains al the information needed for it to fold into its native, fucnal 3-d structure

Gobular proteins are involved in the chemical functions of living things. The ones known as enzymes are organic catalyses that speed up the chemical reaction rates in cells. Other important gobular proteins are hemoglobin, antibodies, and some hormones.

Primary structure

There are four levels of structure in proteins. The simplest is level is called primary structure. It is determined by the kind, number and sequence of amino acids. The amino acids or peptides are joined to one another by strong covalent bonds. These bonds form between the nitrogen atom of the amino group and the oxygen atom of the carboxyl group. They are called peptide bonds.

Secondary structure

The second level of structure involves the coiling of primary chains into a helix or the formation of what are called pleated (beta) sheets Collagen is an example of a pleated sheet. Bonding between sulfhydryl groups of the amino acid cystine forms a strong covalent bond called a disulfide bond. In addition, ionic and weak hydrogen bonds help to stabilize the secondary structure.

Tertiary structure

The third level of protein structure has increased folding between alpha helix and non alpha helix regions. The structure is stabilized by disulfide, ionic, and hydrogen bonding. Gamma gobulin is an example of a gobular protein exhibiting tertiary structure. Keratin is a fibrous protein found in animal hair, claws and fingernails.

Quaternary structure

The final level of protein structure is composed of sub units of polypeptide chains with or without non amino acids. Like the two levels before them they are held together by disulfide, ionic and hydrogen bonding. Hemoglobin exhibits this structure. It is also an example of a conjugated protein because of the presence of a non amino acid group called the "heme group".

Denaturating of a Protein

The term denaturation is used to describe changes in a protein's shape. Such changes maybe temporary or permanent. In either case the breaking of the stabilizing bonds of a protein leads to its inactivation.

Any of the following conditions can bring about the denaturing of a protein:

* heat
* pH
* pressure
* chemicals
* heavy metals

Hydrophobic "Effect"

Other molecules exclude water molecules b/c of organization necessary to deal w/ H-bonds.

Generally, when there's a proline -> ring structure is restrictive to a-helix or b-sheet.

Cooperative Transition

Proteins tend to be either all folded or all unfolded
-> protein placed in condition where some part is thermodynamically unstable: part of folded structure is disrupted -> interact'ns b/w it and remainder of protein are lost -> destabilizes entire protein

Leventhal's Paradox

Difference b/w calculated and actual folding time of a protein
-> Reveals that proteins do not fold by trying every conformation

Cumulative Selection of Protein Folding

* Partly correct intermediates are retained
-> correctness is not based on residues per se, but on total free energy
-> proteins are only marginally stable

Nucleation Condensation Model (Perscht) of Protein Folding

* A difuse folding nucleus is formed & consolidated through the transition state
-> local regions taht have significant structural preference, though not nec. stable on their own, will tend to adopt their favored structure
->interact: increase stability
* Viewed as a funnel: begins w/ highest free energy & many possible conformations; as free energy decreases, so do possible accessible conformations

represents the fcnal expression of information, such as type, fcn, & interactions w/ protein that yield as a fcnal unit

Salting Out (precipitation)

Can be used to fractionate proteins since most are less soluble at high [salt]. This concentration (at which protein is no longer soluble) is diff for diff proteins
-> use [diff] depending on what you want to precipitate

Dialysis

Semipermeable membrane -> proteins too big to leave bag, while small molecules may leave
* useful to get rid of salt, although it won't sep diff proteins

Gel Filtration Chromatography

SIZE: LARGE=FAST, SMALL=SLOW
* gel (such as agarose) contains many beads, large molecules flow around them, small molecules get stuck in them

Proteins containing HIS tags are passed through a column of beads containing covalently attached, immobilized nickel (II) or other metal ions
-> HIS-tag binds tightly to immobilized metal ions, binding desired protein while other proteins flow though the column
* protein eluted by addition of imidazole or another molecule that displaces his

HPLC

* similar to other column techniques but column materials are much finer
-> more interaction sites = greater resolving power
-> pressure added to obtain adeq. flow rate

Gel Electrophoresis

NET CHARGE AND SIZE
* run on polyacrylamide gel

velocity=Ez/f
f-depends on mas and shape and viscosity of medium)
z=charge
E=electric field strength